I have run MToolBox on multiple samples and it has worked effectively for most. However, for some I do not seem to get a VCF file output. It's strange because the logassemble file looks normal to me.
logassemble.txt:
Converting SAM to BAM...
Sorting and indexing BAM...
Creating pileup...
Reading mtDNA sequence...
Reading pileup file...
Assembling...
Basic statistics:
Assembled bases: 100.00%
Mean coverage depth: 7404.76
Number of Contigs: 1
Base composition [A,C,G,T]: 0.31,0.31,0.13,0.25
searching for indels in clone3.. please wait...
searching for mismatches in clone3.. please wait...
I also have VCF_dict_tmp and merged_diff.csv files produced but no VCF_file.vcf. I can see that there should be variants to put into a VCF.
I would greatly appreciate any help.
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Did you check if your VCF_file.vcf has been overwritten by other vcf files? How did you run MToolBox? On a set of samples in the same folder or on separated folders?
However, I think that the log of the complete MToolBox run could help us to understand better your problem.
I have run MToolBox on multiple samples and it has worked effectively for most. However, for some I do not seem to get a VCF file output. It's strange because the logassemble file looks normal to me.
logassemble.txt:
Converting SAM to BAM...
Sorting and indexing BAM...
Creating pileup...
Reading mtDNA sequence...
Reading pileup file...
Assembling...
Basic statistics:
Assembled bases: 100.00%
Mean coverage depth: 7404.76
Number of Contigs: 1
Base composition [A,C,G,T]: 0.31,0.31,0.13,0.25
searching for indels in clone3.. please wait...
searching for mismatches in clone3.. please wait...
I also have VCF_dict_tmp and merged_diff.csv files produced but no VCF_file.vcf. I can see that there should be variants to put into a VCF.
I would greatly appreciate any help.
Dear Tom,
Did you check if your VCF_file.vcf has been overwritten by other vcf files? How did you run MToolBox? On a set of samples in the same folder or on separated folders?
However, I think that the log of the complete MToolBox run could help us to understand better your problem.
PS please, for next issues try to use the mtoolbox google group!
https://groups.google.com/forum/?hl=IT#!forum/mtoolbox-users
Thanks
Claudia
Last edit: Claudia Calabrese 2015-01-23